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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctttaatccctctctcacactcactcacacacacacacacacacgaaacatgcatgcaagactgctgacttagtcaatggtaatctgacattatgttattaatctccagTGAAATCCATATTCCAAGGAATATATCTTGCCCTGTTTCTCCCATTGGAAGCCCACTTTTGAGGTCAAGATCACCACAGCACAGGAATGGGAAAATGTCT

Basic information

species Glycine max
transcript GLYMA20G30100.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G30100.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 11
gtctttaatccctctctcacactcactcacacacacacacacacacgaaacatgcatgcaagactgctgacttagtcaatggtaatctgacattatgttattaatctccagTGAAATCCATATTCCAAGGAATATATCTTGCCCTGTTTCTCCCATTGGAAGCCCACTTTTGAGGTCAAGATCACCACAGCACAGGAATGGGAAAATGTCT
  || |||    |      | |||  |       | | | | |||    |  || ||| |   ||||  |   |       ||| ||| |   |  ||  ||      |||||| || ||| | | |||  ||||||||||||||||||||||   ||| ||||| | | ||||||||||||| ||||| ||    ||||| | |||||| 
--ctataagaaatacagttc-ctcgttttttttaaaaaaaaaacagttca-gtgaatgtatatctgc--atggaaatgtatgtactctaatcatcggtgcttg-----cagTGATATTCATGTACGAAGCTATATATCTTGCCCTGTTTCTCCATGTGGGAGCCCTCATCTGAGGTCAAGATCTCCACAACATCAAAATGGTATAATGTCA
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|18690804|gb|BM519652.1|BM519652
EST:     AGACTTTCTGTTCATTCTTCTAGATTTTTGAAAACTAATCCTCATGAAAG                         TGAAATCCATATTCCAAGGAATATATCTTGCCCTGTTTCTCC
genomic: AGACTTTCTGTTCATTCTTCTAGATTTTTGAAAACTAATCCTCATGAAAGgtctttaatc ... taatctccagTGAAATCCATATTCCAAGGAATATATCTTGCCCTGTTTCTCC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaagactgctgacttagtcaatggtaatctgacattatgttattaatctccagTGAAATCCATATTCCAAGGAATATATCTTGCCCTGTTTCTCCCATTGGAAGCCCACTTTTGAGGTCAAGATCACCACAGCACAGGAATGGGAAAATGTCT
                                          tattaat  putative branch site (score: 2)
                                                tctcc  CT-rich tract
                                 acattatgttattaat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctttaatccctctctcacactcactcacacacacacacacacacgaaacatgcatgcaagactgctgacttagtcaatggtaatctgacattatgttattaatctccagTGAAATCCATATTCCAAGGAATATATCTTGCCCTGTTTCTCCCATTGGAAGCCCACTTTTGAGGTCAAGATCACCACAGCACAGGAATGGGAAAATGTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA